[gmx-users] Problem in starting make hole

[Mark Abraham]

nur avneet wrote:
> Sir
> i want to use makehole program (gromacs 3.1.4)and i used the grompp 
> command on dmpc.pdb with position restraints as specified in the tutorial.
> 
> the position restraint file is as follows :
> [ position_restraints ]
> ; atom  type      fx      fy      fz
>      8     1     0.0     0.0  1000.0
> 
> the tutorial says, this will restraint all phosphorous atoms in the 
> bilayer in z-coordinates.
> What does "type" specify? also, the pdb file has different number for 
> every phosphorous atom of the dmpc molecules. Will specifying only '8' 
> only , restraint all P8s?

Table 5.4 in the manual.

> when i give the grompp command i get the following error:
> .
> .
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> calling /lib/cpp...
> cecmel311334_hole_dmpc.top:11:1: error: unterminated #else
> cpp exit code: 256
> Tried to execute: '/lib/cpp  -I/usr/local/gromacs/share/top -DPOSRES 
> cecmel311334_hole_dmpc.top > gromppZOiO4o'
> The '/lib/cpp' command is defined in the .mdp file
> processing topology...
> Generated 1174 of the 2016 non-bonded parameter combinations
> Cleaning up temporary file gromppZOiO4o
> Fatal error: [ file "lipid_posre.itp", line 3 ]:
>              Atom index (8) in position_restraints out of bounds (1-3)
> 
> What does this mean? n please guide how to proceed..

That means you're trying to restrain atom number 8 in a molecule that 
has only 3 atoms. Read section 5.6.1 to work out how you managed to do this.

Mark